Contacts of the helix formed by residues 684 - 699 (chain F) in PDB entry 5A31
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 684 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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655F GLU* 3.9 26.9 + - - +
679F GLN* 3.1 20.6 + - + +
682F LEU* 3.4 12.9 - - + +
683F LYS* 1.3 73.6 - - - +
685F SER* 1.3 58.3 + - - +
686F GLU* 3.3 4.5 - - - -
687F LYS* 3.3 42.7 + - + +
688F ALA* 3.0 25.5 + - - +
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Residues in contact with SER 685 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680F HIS* 4.3 22.9 - - - +
683F LYS* 3.0 13.7 + - - +
684F LYS* 1.3 72.7 - - - +
686F GLU* 1.3 75.6 + - - +
688F ALA* 3.2 9.5 + - - +
689F LEU* 2.9 24.9 + - - +
712F VAL* 4.4 3.2 - - - +
716F ASN* 3.8 27.0 + - - -
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Residues in contact with GLU 686 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683F LYS 4.6 1.9 - - - +
684F LYS* 3.3 1.8 - - - -
685F SER* 1.3 89.6 + - - +
687F LYS* 1.3 63.3 + - + +
689F LEU* 3.5 7.2 + - - +
690F ASP* 3.1 30.8 + - - +
716F ASN* 6.0 1.6 - - - +
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Residues in contact with LYS 687 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679F GLN* 3.9 9.6 - - - +
684F LYS* 3.3 42.9 + - + +
685F SER 3.3 0.2 - - - -
686F GLU* 1.3 79.0 - - + +
688F ALA* 1.3 64.6 + - - +
690F ASP* 3.1 14.8 + - - +
691F THR* 2.9 24.7 + - - +
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Residues in contact with ALA 688 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676F GLY* 3.4 23.7 - - - +
679F GLN* 3.6 12.9 + - - -
680F HIS* 3.5 26.2 - - + +
684F LYS 3.0 10.3 + - - +
685F SER 3.3 9.4 - - - +
687F LYS* 1.3 75.8 - - - +
689F LEU* 1.3 64.3 + - - +
691F THR* 3.0 3.9 + - - -
692F LEU* 2.9 28.2 + - - +
712F VAL* 4.7 6.5 - - + -
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Residues in contact with LEU 689 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685F SER 2.9 15.3 + - - +
686F GLU* 4.0 6.5 - - - +
688F ALA* 1.3 76.0 - - - +
690F ASP* 1.3 59.7 + - - +
692F LEU* 4.5 3.1 - - - -
693F ASN* 2.9 34.3 + - + +
709F ARG* 3.7 41.3 - - + +
712F VAL* 4.0 15.0 - - + +
713F LEU* 4.0 27.1 - - + -
716F ASN* 4.4 9.4 - - - +
718F LYS* 4.1 16.6 - - - +
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Residues in contact with ASP 690 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686F GLU* 3.1 19.3 + - - +
687F LYS* 3.1 19.2 + - - +
689F LEU* 1.3 80.6 - - - +
691F THR* 1.3 61.6 + - - +
693F ASN* 3.5 8.6 - - - +
694F LYS* 3.3 27.4 + - + +
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Residues in contact with THR 691 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672F LEU* 3.4 44.2 - - + +
675F ILE* 4.0 7.6 - - + -
676F GLY* 3.8 11.2 - - - +
679F GLN* 2.9 24.2 + - - -
687F LYS* 2.9 10.4 + - - +
688F ALA 3.0 7.8 + - - -
690F ASP* 1.3 76.2 - - - +
692F LEU* 1.3 63.9 + - - +
694F LYS* 3.1 25.9 + - - +
695F ALA* 3.2 11.1 + - - +
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Residues in contact with LEU 692 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672F LEU 5.3 0.4 - - - -
673F CYS* 4.1 22.4 - - - +
676F GLY* 4.4 18.6 - - - -
677F VAL* 4.8 0.7 - - + +
688F ALA 2.9 17.1 + - - +
689F LEU* 3.9 4.0 - - - +
691F THR* 1.3 74.5 - - - +
693F ASN* 1.3 65.7 + - - +
695F ALA* 3.1 16.2 + - - +
696F ILE* 3.3 16.1 + - - +
705F CYS* 3.4 28.7 - - - +
708F HIS* 3.7 25.1 - - + +
709F ARG* 4.0 15.3 - - + +
712F VAL* 3.5 33.0 - - + -
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Residues in contact with ASN 693 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689F LEU* 2.9 20.8 + - + +
690F ASP* 3.5 10.1 - - - +
692F LEU* 1.3 76.5 - - - +
694F LYS* 1.3 61.5 + - - +
696F ILE* 3.2 15.1 + - - +
697F VAL* 3.4 20.0 + - - +
709F ARG* 3.0 35.8 + - - +
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Residues in contact with LYS 694 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662F LEU* 5.1 6.1 - - - +
672F LEU* 4.2 26.6 - - + +
690F ASP* 3.3 16.6 + - + +
691F THR* 3.1 16.0 + - - +
693F ASN* 1.3 76.4 - - + +
695F ALA* 1.3 66.9 + - - +
697F VAL* 3.1 10.3 + - - +
698F ILE* 2.9 35.9 + - + +
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Residues in contact with ALA 695 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669F SER* 4.0 12.5 - - - +
672F LEU* 3.7 32.5 - - + +
673F CYS* 4.1 14.8 - - - -
691F THR 3.2 4.6 + - - +
692F LEU* 3.1 14.3 + - - +
694F LYS* 1.3 80.5 - - - +
696F ILE* 1.3 61.8 + - - +
698F ILE* 3.4 3.4 + - - +
699F ASP 3.1 10.7 + - - -
702F ASN* 2.9 20.7 + - - -
705F CYS* 4.1 3.8 - - + -
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Residues in contact with ILE 696 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692F LEU 3.3 7.6 + - - +
693F ASN* 3.2 7.7 + - - +
694F LYS 3.2 0.8 - - - -
695F ALA* 1.3 76.2 - - - +
697F VAL* 1.3 62.4 + - + +
699F ASP 2.8 23.9 - - - +
700F PRO* 3.9 3.5 - - + +
701F LYS 5.2 3.8 - - - +
705F CYS* 3.1 28.7 - - - -
706F LYS* 4.1 26.7 - - - +
709F ARG* 3.4 44.0 - - + +
725F GLU* 3.5 12.1 - - - +
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Residues in contact with VAL 697 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693F ASN* 3.6 20.6 - - - +
694F LYS* 3.1 10.0 + - - +
696F ILE* 1.3 80.9 - - + +
698F ILE* 1.3 65.8 + - + +
699F ASP* 3.5 2.1 + - - -
700F PRO* 4.5 5.0 - - - +
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Residues in contact with ILE 698 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482F LYS* 5.1 4.5 + - - -
667F GLN* 3.3 56.1 + - + +
669F SER* 4.6 5.2 - - - +
672F LEU* 3.6 26.2 - - + -
694F LYS* 2.9 27.1 + - + +
695F ALA* 3.9 5.8 - - - +
697F VAL* 1.3 81.7 - - + +
699F ASP* 1.3 69.1 + - - +
700F PRO* 4.0 3.9 - - - +
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Residues in contact with ASP 699 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482F LYS* 4.5 9.7 + - - -
512F LEU* 5.3 10.0 - - - +
513F SER* 6.2 0.2 - - - -
667F GLN* 4.0 16.8 + - - +
669F SER* 3.0 25.8 + - - +
695F ALA 3.1 6.5 + - - -
696F ILE* 2.8 16.3 - - - +
698F ILE* 1.3 85.6 - - - +
700F PRO* 1.4 68.1 - - + +
701F LYS 3.4 1.0 + - - -
702F ASN* 2.8 43.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il